Biofuel expansion efforts and climate mitigation policy could fundamentally alter land management trends in U.S. agriculture and forestry (AF) by mandating biofuel feedstock production and providing incentives for greenhouse gas (GHG) emissions reduction and carbon sequestration from terrestrial sources. Research has shown that biofuel expansion can alter commodity markets, induce agricultural land expansion, and intensify production. Meanwhile, GHG mitigation efforts could limit agricultural expansion, reduce current cultivation, and lower management intensity by incentivizing GHG emissions reduction and carbon sequestration within AF. To date, little work has attempted to quantify biofuel and climate policy-induced shifts together along the extensive and intensive agricultural production margins within a systems-based framework, though such shifts could have resounding implications on agricultural water consumption and quality. This study uses a comprehensive and detailed economic model of the U.S. AF sectors to simulate land management responses to biofuel expansion and GHG policies. While bioenergy production and altered AF management practices are found to significantly reduce GHG emissions, additional water consumption and nutrient use are possible policy outcomes. Specifically, we find that policies that influence shifts to the extensive margin will increase aggregate water use and nutrient application, but lead to lower intensity per-unit area. Conversely, when combined with biofuel mandates climate mitigation incentives lower agricultural land expansion, but lead to higher levels of management intensity. Somewhat contrary to expectations, GHG mitigation incentives cause water and nutrient use intensity to grow at an increasing rate due to the greater level of land use competition. Additionally, important regional trends emerge, as water use and quality concerns grow with the CO2 price in areas with limited GHG mitigation possibilities. This suggests that “water leakage” is possible whereby emissions reduction activities decrease output in one region and stimulate management intensity elsewhere. The potential indirect consequences of combined biofuel and climate mitigation incentives on water resource systems warrant further attention in policy design and future research.